_quarto.yml

project:
  title: KIMMDY
  type: website
  output-dir: docs
  render:
    - index.qmd
    - _reference
    - guide
  resources:
    - objects.txt


website:
  favicon: ./www/favicon.png
  page-navigation: true
  site-url: http://graeter-group.github.io/kimmdy
  repo-url: https://github.com/graeter-group/kimmdy
  repo-actions: [edit, issue]
  reader-mode: true
  back-to-top-navigation: true
  navbar:
    background: light
    tools:
      - icon: github
        menu:
          - text: Source Code
            url:  https://github.com/graeter-group/kimmdy
          - text: Report a Bug
            url:  https://github.com/graeter-group/kimmdy/issues/new
    left:
      - file: ./guide/tutorials/getting-started.qmd
        text: Getting Started
      - file: ./guide/how-to/index.qmd
        text: How-To
      - file: ./guide/tutorials/index.qmd
        text: Tutorials
      - file: ./guide/explanation/index.qmd
        text: Explanations
      - file: _reference/index.qmd
        text: Reference
  sidebar:
    logo: ./www/kimmdy_logo.png
    subtitle: "Reactive MD pipeline for GROMACS using Kinetic Monte Carlo / Molecular Dynamic"
    style: "floating"
    collapse-level: 1
    contents:
      - text: KIMMDY
        file: index.qmd
      - section: Tutorials
        contents: guide/tutorials/**
      - section: How-To
        contents: guide/how-to/**
      - section: Explanation
        contents: guide/explanation/**
      - section: Reference
        href: _reference/index.qmd
        contents:
        - guide/references/input.qmd
        - guide/references/cmd_ref.qmd
        - section: Python API
          contents:
            - _reference/cmd.qmd
            - contents:
              - _reference/topology.topology.qmd
              - _reference/topology.ff.qmd
              - _reference/topology.utils.qmd
              - _reference/topology.atomic.qmd
              - _reference/parsing.TopologyDict.qmd
              section: Topology
            - contents:
              - _reference/homolysis.reaction.Homolysis.qmd
              - _reference/hat_naive.reaction.NaiveHAT.qmd
              - _reference/dummyreaction.reaction.DummyReaction.qmd
              section: Reaction Plugins
            - contents:
              - _reference/constants.qmd
              - _reference/coordinates.qmd
              - _reference/config.qmd
              - _reference/kmc.qmd
              - _reference/parsing.qmd
              - _reference/runmanager.qmd
              - _reference/tasks.qmd
              - _reference/recipe.qmd
              - _reference/plugins.qmd
              - _reference/analysis.qmd
              - _reference/utils.qmd
              - _reference/tools.qmd
              section: Other Modules

# metadata-files:
#   - _sidebar.yml

execute:
  warning: false
  echo: true
  freeze: auto

format:
  html:
    toc: true
    toc-depth: 5
    toc-expand: true
    mainfont: Roboto
    number-depth: 0
    highlight-style: arrow
    theme:
      light:
      - www/theme.scss
      dark:
      - www/theme.scss
      - www/theme-dark.scss
    code-copy: true

filters:
  - interlinks

interlinks:
  fast: true
  sources:
    numpy:
      url: https://numpy.org/doc/stable/
    python:
      url: https://docs.python.org/3.10/

quartodoc:
  sidebar: "_sidebar.yml"
  render_interlinks: true
  title: "References"
  package: kimmdy
  style: pkgdown
  dir: _reference
  sections:
    - title: Input file
      desc: "[Options of the main KIMMDY input file](/guide/references/input.qmd)"
    - title: Command Line Interface
      desc: "[Arguments of all KIMMDY parts.](../guide/references/cmd_ref.qmd)"
    - title: Python API
      desc: Start KIMMDY from a python script or the command line
      contents:
        - name: cmd
    - title: Topology
      desc: Topology modules
      contents:
        - name: topology.topology
        - name: topology.ff
        - name: topology.utils
        - name: topology.atomic
        - name: parsing.TopologyDict
    - title: Modules
      desc: Modules
      contents:
        - name: analysis
        - name: cmd
        - name: config
        - name: constants
        - name: coordinates
        - name: kmc
        - name: parsing
        - name: plugins
        - name: recipe
        - name: runmanager
        - name: schema
        - name: tasks
        - name: tools
        - name: utils
    - title: Reaction Plugins
      desc: Reaction plugins bundled with KIMMDY and the protocol to add a new reaction plugin to KIMMDY
      package: null
      contents:
        - homolysis.reaction.Homolysis
        - hat_naive.reaction.NaiveHAT
        - dummyreaction.reaction.DummyReaction